Guianacara cuyunii belongs to the subgenus Guianacara and it differs from G. oelemariensis (subgenus Oelemaria) by having 2 supraneurals instead of one and by possessing a uniformly dark midlateral bar, in contrast with a midlateral spot. It can be distinguished from G. stergiosi, G. geayi and G. sphenozona in having a thinner midlateral bar which is three scales at its widest point, gradually thinning to two scales below the lateral line (vs. midlateral bar four scales at its widest and is never thinned to less than three scales). Adult G. cuyunii retain the black coloration in the membranes of the anterior three dorsal spines (lost in adults of G. sphenozona and G. geayi). It is distinguished from G. owroewefi by its thinner, never faint midlateral bar. Furthermore, G. cuyunii can be distinguished from G. stergiosi, G. owroewefi, and G. sphenozona by having a pectoral fin that does not reach the base of the anal fin and a branchiostegal membrane of background body color instead of dusky (Ref. 57436).